Tomato Yellow Leaf Curl Virus Research Articles

Plant resistance to tomato yellow leaf curl virus is enhanced by Bacillus amyloliquefaciens Ba13 through modulation of RNA interference.

Tomato yellow leaf curl virus (TYLCV), which is a typical member of the genus Begomovirus, causes severe crop yield losses worldwide. RNA interference (RNAi) is an important antiviral defense mechanism in plants, but whether plant beneficial microbes used as biocontrol agents would modulate RNAi in defense against TYLCV remains unclear. Here, we employed whole-transcriptome, bisulfite, and small RNA sequencing to decipher the possible role of Bacillus amyloliquefaciens Ba13 as a bacterial biocontrol agent against TYLCV in RNAi modulation. Potted tomato plants were exposed to whiteflies for natural viral infection 14 days after bacterial inoculation. Compared with non-inoculated controls, the abundance of TYLCV gene in the leaves of inoculated plants decreased by 70.1% at 28 days post-infection, which mirrored the pattern observed for plant disease index. The expression of the ARGONAUTE family genes (e.g., AGO3, AGO4, AGO5, and AGO7) involved in antiviral defense markedly increased by 2.44-6.73-fold following bacterial inoculation. The methylation level at CpG site 228 (in the open reading frame region of the RNA interference suppressing gene AV2) and site 461 (in the open reading frame regions of AV1 and AV2) was 183.1 and 63.0% higher in inoculated plants than in non-inoculated controls, respectively. The abundances of 10 small interfering RNAs matched to the TYLCV genome were all reduced in inoculated plants, accompanied by enhancement of photosystem and auxin response pathways. The results indicate that the application of Ba. amyloliquefaciens Ba13 enhances plant resistance to TYLCV through RNAi modulation by upregulating RNAi-related gene expression and enhancing viral genome methylation.

Physiology and Gene Expression Analysis of Tomato (Solanum lycopersicum L.) Exposed to Combined-Virus and Drought Stresses.

Crop productivity can be obstructed by various biotic and abiotic stresses and thus these stresses are a threat to universal food security. The information on the use of viruses providing efficacy to plants facing growth challenges owing to stress is lacking. The role of induction of pathogen-related genes by microbes is also colossal in drought-endurance acquisition. Studies put forward the importance of viruses as sustainable means for defending plants against dual stress. A fundamental part of research focuses on a positive interplay between viruses and plants. Notably, the tomato yellow leaf curl virus (TYLCV) and tomato chlorosis virus (ToCV) possess the capacity to safeguard tomato host plants against severe drought conditions. This study aims to explore the combined effects of TYLCV, ToCV, and drought stress on two tomato cultivars, Money Maker (MK, UK) and Shalala (SH, Azerbaijan). The expression of pathogen-related four cellulose synthase gene families (CesA/Csl) which have been implicated in drought and virus resistance based on gene expression analysis, was assessed using the quantitative real-time polymerase chain reaction method. The molecular tests revealed significant upregulation of Ces-A2, Csl-D3,2, and Csl-D3,1 genes in TYLCV and ToCV-infected tomato plants. CesA/Csl genes, responsible for biosynthesis within the MK and SH tomato cultivars, play a role in defending against TYLCV and ToCV. Additionally, physiological parameters such as "relative water content," "specific leaf weight," "leaf area," and "dry biomass" were measured in dual-stressed tomatoes. Using these features, it might be possible to cultivate TYLCV-resistant plants during seasons characterized by water scarcity.

A New Strategy of Cross-Protection Based on Attenuated Vaccines: RNA Viruses Are Used as Vectors to Control DNA Viruses

Plant viruses can infect various types of plants, including food and oil crops, and ornamental flowers, threatening agricultural production and food supply. Cross-protection is an efficient strategy against severe viral strains. Due to distinct infection mechanisms, cross-protection cases involving RNA viruses and DNA viruses often rely on the utilization of corresponding attenuated strains for control purposes. In this study, we utilized cucumber mosaic virus (CMV), a member of the RNA virus group, as the foundational framework for developing attenuated vaccines. We developed four vaccines by inserting relevant sequences from tomato yellow leaf curl virus (TYLCV), a DNA virus. All vaccines demonstrated effective prevention against TYLCV infection, with relative control efficacies exceeding 80%. Subsequently, we evaluated the preventive effects of these vaccines on mixed infections of CMV and TYLCV. Our findings demonstrated that CMV (R2-2bPTI-TYC1C4), CMV (R2-2bPTII-TYC1C4), and CMV (R2-2bPTIII-TYRep) displayed significant efficacy in preventing mixed infections. Following pre-inoculation with these vaccines, the disease index of tomato plants decreased from 100 to 56. This work provides theoretical foundations and tangible resources for controlling TYLCV through cross-protection while suggesting a feasible strategy for utilizing weak RNA virus vaccines to control DNA viruses.

Molecular detection of Pepper yellow leaf curl virus, Tomato leaf curl virus, Tomato yellow leaf curl virus, and Mungbean yellow mosaic virus on eggplant, tomato, and pepper at different altitudes in East Java, Indonesia

The genus Begomovirus causes yellow disease is the most damaging and threatening for eggplant, tomato, and pepper production worldwide. Begomoviruses (Family Geminiviridae) are transmitted circulative persistent manner by Bemisia tabaci. This study aims to determine the variation of infection of several species of Begomoviruses in tomato, eggplant, and pepper at different altitudes in East Java. Molecular detection of infection Begomoviruses were discovered using PCR and four pairs of specific primers. Samples were collected at different altitudes in East Java (Kencong, Karangploso, and Pujon). The PCR was successfully applied to detect Pepper yellow leaf curl virus, Tomato leaf curl virus, and Tomato yellow leaf curl virus from tomato, eggplant, and pepper in Kencong. Tomato, eggplant, and pepper from all locations were not infected by Mungbean yellow mosaic virus. Symptoms of Begomovirus infection found in the samples from Kencong were more varied than those found in Karangploso and Pujon. The phylogenetic analysis’ findings revealed that the TYLCV Kencong shared the highest homologies with TYLCKaV pepper and eggplant from Indonesia; PepYLCV Kencong shared with PepYLCV Ageratum conyzoides from Indonesia; and ToLCV Kencong shared with ToLCNDV cucumber from Central Java. The molecular detection has shown that there are different combinations of Begomovirus infection at altitudes.

Association of Tomato Chlorosis Virus Complicates the Management of Tomato Yellow Leaf Curl Virus in Cultivated Tomato (Solanum lycopersicum) in the Southern United States

Tomato (Solanum lycopersicum L.) production in the USA has been severely impacted by the tomato yellow leaf curl virus (TYLCV). Furthermore, a complex association of whitefly-transmitted TYLCV (genus, begomovirus) and tomato chlorosis virus (ToCV, genus, crinivirus) were recently identified in tomato. Several tomato cultivars were developed and commercialized with intermediate resistance (IR) against TYLCV-IL (Israel), the predominant strain of TYLCV found in Georgia, USA. TYLCV-resistant cultivars were tested in open field conditions against multiple whitefly-transmitted viruses in Georgia under natural disease pressure during the fall of 2022. The area under disease progress curve (AUDPC) over time showed a steady increase in disease severity among all cultivars. Further analysis of infected samples using high throughput sequencing (HTS) and quantitative PCR (qPCR) revealed the presence of TYLCV and ToCV in symptomatic upper and lower leaves, respectively. Moreover, the presence of both viruses in upper and lower leaves was determined. A mixed infection of both viruses, TYLCV and ToCV, resulted in severe disease development which may enhance the commercial tomato plants to break resistance and lead to decreased fruit quality and marketable yields.

Ecoepidemiological Model and Optimal Control Analysis of Tomato Yellow Leaf Curl Virus Disease in Tomato Plant

The purpose of this study is to analyze the impact of control strategies, namely, insecticide spray, roguing of a diseased tomato plant, and protective netting to protect tomato plant from tomato yellow leaf curl virus disease (TYLCVD). For this, we formulate and analyze a simple deterministic model for the transmission dynamics of TYLCVD that incorporates these control strategies. We initially take into account the constant control case, we calculate the basic reproduction number, and we investigate the existence and stability of the disease-free and endemic equilibria. We use the Kamgang-Sallet stability to ensure that the disease-free equilibrium point is globally asymptotically stable when the reproduction number R 0 is less than one. This indicates that TYLCVD dies out independent of the initial size of the tomato population. For R 0 < 1 , the disease-free equilibrium becomes unstable, and the endemic equilibrium is globally asymptotically stable. This indicates that TYLCVD propagates. In the nonconstant control case, we use Pontryagin’s maximum principle to derive the necessary conditions for the optimal control of the disease. Our findings show that all the combined efforts of two out of three strategies can significantly reduce the power of infectivity of the disease except the combination of the use of insecticide spray and rouging infected tomato plants. Besides our numerical simulations show, the implementation of the combination of roguing diseased plants and protective netting has a similar effect in minimizing or eliminating TYLCV as the use of all strategies. Hence, as resources are always in scarce, we recommend policymakers to adapt the combination of the use of roguing diseased tomato plants and protective netting to eradicate the disease.

Utilizing genetic diversity to select tomato lines tolerant of tomato yellow leaf curl virus based on genotypic coefficient of variation, heritability, genotypic correlation, and multivariate analyses

Tomato yellow leaf curl virus (TYLCV) is one of the most destructive pathogens for tomato crops. The development of TYLCV-tolerant tomato lines (TLs) requires a thorough understanding of their genetic variability and relationships among lines and in traits of interest. Twelve F9 TLs were evaluated for phenotypic TYLCV tolerance, vegetative growth, yield, and fruit quality during the 2018 and 2019 fall seasons to identify elite breeding lines. TLs were selected by a bulk selection method from segregating generations of the commercial F1 hybrids TH99802 (TLs 1–6) and TH99806 (TLs 7–12). TLs exhibited either mild or no symptoms. The TYLCV titer varied between 0.8 × 105 and 3.9 × 105 in symptomless TLs plants compared to 56.7 × 105 in severely symptomatic plants of susceptible ‘Castlerock.’ Across both seasons, TL-3, TL-5, and TL-8 exhibited the highest total and marketable plant yields, TYLCV tolerance, and acceptable fruit quality. Most traits had high estimates of genetic variance, genotypic coefficient of variance, and broad sense heritability. Our results indicated that there was sufficient genetic variability for selection of the best lines. Principal component analysis and hierarchical cluster analysis indicated that the TLs were highly diverse of the evaluated traits and could be divided into three clusters. Cluster 1, which included TL-1, TL-3, and TL-8, performed better for TYLCV tolerance and economically important traits. Clusters 1 and 2 showed the greatest degree of dissimilarity. Therefore, crossing parents from Cluster 1 with 2 is predicated to maximum recombination for improve genotypes.

Phylogenomic and population genetics analyses of extant tomato yellow leaf curl virus strains on a global scale

Tomato yellow leaf curl virus (TYLCV) is a monopartite DNA virus with a genome size of ~ 2,800 base pairs. The virus belongs to the genus Begomovirus within the family Geminiviridae. Extant TYLCV strains are differentiated based on an established threshold of 94% genome-wide pairwise nucleotide identity. The phylogenetic relationships, diversification mechanisms, including recombination, and extent of spread within and from the center of origin for TYLCV have been reported in previous studies. However, the evolutionary relationships among strains, strains’ distribution and genomic diversification, and genetic mechanisms shaping TYLCV strains’ evolution have not been re-evaluated to consider globally representative genome sequences in publicly available sequence database, including herein newly sequenced genomes from the U.S. and Middle East, respectively. In this study, full-length genome sequences for the extant strains and isolates of TYLCV (n=818) were downloaded from the GenBank database. All previously published genome sequences, and newly sequenced TYLCV genomes of TYLCV isolates from Kuwait and USA, determined herein (n=834), were subjected to recombination analysis. To remove the ‘phylogenetic noise’ imparted by interspecific recombination, the recombinant genomes were removed from the data set, and the remaining non-recombinant genome sequences (n=423) were subjected to population genetics and Bayesian analyses. Results of the phylogeographical analysis indicated that the type strain, TYLCV-Israel, and TYLCV-Mild strain, were globally distributed, spanning Africa, America, Asia, Australia/Oceania, Europe, and New Caledonia, while the other TYLCV strains were prevalent only throughout the Middle East. The results of Bayesian evolutionary (ancestral) analysis predicted that TYLCV-Israel represents the oldest, most recent common ancestor (MRCA) (41,795 years), followed by TYLCV-Mild at 39,808 years. These were closely followed by two Iranian strains viz., TYLCV-Kerman and TYLCV-Iran at 37,529 and 36,420 years, respectively. In contrast, the most recently evolving strains were TYLCV-Kuwait and TYLCV-Kahnooj at 12,445 and 298 years, respectively. Results of the neutrality test indicated that TYLCV-Israel and TYLCV-Mild populations are undergoing purifying selection and/or population expansion, although statistically significant selection was documented for only TYLCV-Israel, based on positive selection acting on five codons.

Divergent Responses of Tomato Cultivars with Resistance to Tomato Yellow Leaf Curl Virus as Infected by Meloidogyne javanica

Commercial tomatoes are usually complex F1 hybrids with multiple resistances genes from different wild Solanum species. The response of tomato cultivars with resistance to root-knot nematodes (RKN) and Tomato yellow leaf curl virus (TYLCV) as infected by Meloidogyne javanica was determined in a controlled environment and field conditions. Four treatments were tested, viz. tomato cultivars with (i) RKN resistance alone; (ii) combination of RKN and TYLCV resistance (RKN + TYLCV); (iii) TYLCV resistance alone; and (iv) control (susceptible to the nematode and virus). The RKN-resistant plants effectively suppressed nematode infection and reproduction both in a controlled environment and in field conditions. The RKN + TYLC-resistant plants were less effective (p < 0.001) than the RKN plants in a controlled environment, and their resistance levels were significantly reduced in the field. Nonetheless, the RKN + TYLCV plants supported lower (p < 0.001) nematode infection and reproduction than the susceptible control plants. The TYLCV-resistant plants reduced (p < 0.001) nematode infection and reproduction compared to the susceptible control in a controlled environment and in field conditions. The divergent response of tomato cultivars with resistance to TYLCV via infection by M. javanica can be attributed to the genetic background of the cultivars.

Acylsugar tomato lines suppress whiteflies and Amblyseius swirskii establishment

AbstractPlant defense traits such as trichomes along with biocontrol agents may provide alternatives to insecticide use in tomatoes, Solanum lycopersicum L. (Solanaceae). However, plant‐herbivore‐natural enemy interactions are not always complementary. In a series of greenhouse and field experiments, we explored whether augmented defense traits (i.e., production of acylsugars) in tomato plants could reduce sweet potato whitefly, Bemisia tabaci Gennadius (Hemiptera: Aleyrodidae), populations and aid the establishment of the predatory mite Amblyseius swirskii Athias‐Henriot (Acari: Phytoseiidae). In the field experiment, commercial tomato cultivars and acylsugar‐producing tomato lines received no predatory mites or mites released via three methods: dusting on top, dusting on bottom, or slow‐release sachets. In the first greenhouse experiment, predatory mites were released onto the commercial and acylsugar‐producing tomato plants via sachets. In the second greenhouse experiment using a similar design, we augmented the mite diet with an alternative non‐prey resource (i.e., cattail pollen). Our results indicated that acylsugar‐producing tomato plants supported significantly fewer whiteflies than the commercial lines in all experiments. However, in the field, despite lower whitefly numbers, Tomato yellow leaf curl virus (TYLCV) (Geminiviridae, Begomovirus) was detected at higher frequencies in acylsugar‐producing lines. Few mites were recovered from all commercial and acylsugar‐producing lines in the field or greenhouse experiments suggesting A. swirskii does not establish well on tomatoes, and acylsugar lines successfully decreased whitefly populations but not a viral disease transmitted even at low whitefly abundance.

Genome of Tomato Yellow Leaf Curl Virus (TYLCV) Obtained from Tomato Leaves in Kuwait.

We report here the genome sequence of tomato yellow leaf curl virus (TYLCV) Wafra 19, isolated in Kuwait from symptomatic tomato plant leaves. The genome showed 98.42% identity to the AZ23-1 strain genome sequence.

Begomovirus diversity in tomato crops in Costa Rica

AbstractBegomoviruses (Geminiviridae family) are characterized by their high recombination rate and a wide range of hosts, making their control difficult. In Costa Rica, various species of bipartite begomoviruses have been reported, which are Pepper golden mosaic virus (PepGMV), Tomato yellow mottle virus (ToYMoV), Tomato leaf curl Sinaloa virus (ToLCSiV) and the monopartite begomovirus Tomato yellow leaf curl virus (TYLCV). Since the TYLCV first report in Costa Rica, neither additional knowledge has been produced on how this begomovirus has spread in the country's territory nor on the distribution of the other bipartite species. A total of 429 tomato samples collected during the years 2015–2016 were used to study these aspects. Each sample was georeferenced and analysed with various techniques such as nucleic acid hybridization, polymerase chain reaction (PCR) and sequencing for the begomoviruses previously reported in Costa Rica. It was found that the presence/absence of the different species can vary, depending on the province. TYLCV is present in the six provinces analysed in this work, with a proportion from 3.7 to 86.6 per cent. Alajuela, Cartago, and Heredia are the provinces most affected by tomato‐infecting begomoviruses. Fourteen different haplotypes of TYLCV were detected, but all were identified as TYLCV‐IL. The distribution of TYLCV was related to the presence of the whitefly Bemisia tabaci MED, especially in the country's main tomato production areas. This information allows the phytosanitary surveillance services to develop strategies for the integrated management of the disease and to contribute data to the genetic improvement programmes of the crop.

Phylogenomic and population genetics analyses of extant Tomato yellow leaf curl virus strains on a global scale

Phylogenomic and population genetics analyses of extant Tomato yellow leaf curl virus strains on a global scale

Retraction Note to: Inhibition of Tomato Yellow Leaf Curl Virus (TYLCV) using whey proteins

Retraction Note to: Inhibition of Tomato Yellow Leaf Curl Virus (TYLCV) using whey proteins

Functional identification of a novel C7 protein of tomato yellow leaf curl virus

Tomato yellow leaf curl virus (TYLCV) is a monopartite geminivirus, and one of the most devastating plant viruses in the world. TYLCV is traditionally known to encode six viral proteins in bidirectional and partially overlapping open reading frames (ORFs). However, recent studies have shown that TYLCV encodes additional small proteins with specific subcellular localizations and potential virulence functions. Here, a novel protein named C7, encoded by a newly-described ORF in the complementary strand, was identified as part of the TYLCV proteome using mass spectrometry. The C7 protein localized to the nucleus and cytoplasm, both in the absence and presence of the virus. C7 was found to interact with two other TYLCV-encoded proteins: with C2 in the nucleus, and with V2 in the cytoplasm, forming conspicuous granules. Mutation of C7 start codon ATG to ACG to block the translation of C7 delayed the onset of viral infection, and the mutant virus caused milder virus symptoms and less accumulations of viral DNAs and proteins. Using the potato virus X (PVX)-based recombinant vector, we found that ectopic overexpression of C7 resulted in more severe mosaic symptoms and promoted a higher accumulation of PVX-encoded coat protein in the late virus infection stage. In addition, C7 was also found to inhibit GFP-induced RNA silencing moderately. This study demonstrates that the novel C7 protein encoded by TYLCV is a pathogenicity factor and a weak RNA silencing suppressor, and that it plays a critical role during TYLCV infection.

Geminivirus C5 proteins mediate formation of virus complexes at plasmodesmata for viral intercellular movement.

Movement proteins (MPs) encoded by plant viruses deliver viral genomes to plasmodesmata (PD) to ensure intracellular and intercellular transport. However, how the MPs encoded by monopartite geminiviruses are targeted to PD is obscure. Here, we demonstrate that the C5 protein of tomato yellow leaf curl virus (TYLCV) anchors to PD during the viral infection following trafficking from the nucleus along microfilaments in Nicotiana benthamiana. C5 could move between cells and partially complement the traffic of a movement-deficient turnip mosaic virus (TuMV) mutant (TuMV-GFP-P3N-PIPO-m1) into adjacent cells. The TYLCV C5 null mutant (TYLCV-mC5) attenuates viral pathogenicity and decreases viral DNA and protein accumulation, and ectopic overexpression of C5 enhances viral DNA accumulation. Interaction assays between TYLCV C5 and the other eight viral proteins described in TYLCV reveal that C5 associates with C2 in the nucleus and with V2 in the cytoplasm and at PD. The V2 protein is mainly localized in the nucleus and cytoplasmic granules when expressed alone; in contrast, V2 forms small punctate granules at PD when co-expressed with C5 or in TYLCV-infected cells. The interaction of V2 and C5 also facilitates their nuclear export. Furthermore, C5-mediated PD localization of V2 is conserved in two other geminiviruses. Therefore, this study solves a long-sought-after functional connection between PD and the geminivirus movement and improves our understanding of geminivirus-encoded MPs and their potential cellular and molecular mechanisms.

Large Artificial microRNA Cluster Genes Confer Effective Resistance against Multiple Tomato Yellow Leaf Curl Viruses in Transgenic Tomato.

Tomato yellow leaf curl disease (TYLCD) has become the key limiting factor for the production of tomato in many areas because of the continuous infection and recombination of several tomato yellow leaf curl virus (TYLCV)-like species (TYLCLV) which produce novel and destructive viruses. Artificial microRNA (AMIR) is a recent and effective technology used to create viral resistance in major crops. This study applies AMIR technology in two ways, i.e., amiRNA in introns (AMINs) and amiRNA in exons (AMIEs), to express 14 amiRNAs targeting conserved regions in seven TYLCLV genes and their satellite DNA. The resulting pAMIN14 and pAMIE14 vectors can encode large AMIR clusters and their function in silencing reporter genes was validated with transient assays and stable transgenic N. tabacum plants. To assess the efficacy of conferring resistance against TYLCLV, pAMIE14 and pAMIN14 were transformed into tomato cultivar A57 and the resulting transgenic tomato plants were evaluated for their level of resistance to mixed TYLCLV infection. The results suggest that pAMIN14 transgenic lines have a more effective resistance than pAMIE14 transgenic lines, reaching a resistance level comparable to plants carrying the TY1 resistance gene.

Transcription start site mapping of geminiviruses using the in vitro cap-snatching of a tenuivirus

Geminiviruses are a family of single-stranded DNA viruses that cause significant yield losses in crop production worldwide. Transcription start site (TSS) mapping is crucial in understanding the gene expression mechanisms of geminiviruses. However, this often requires costly and laborious experiments. Rice stripe virus (RSV) has a mechanism called cap-snatching, whereby it cleaves cellular mRNAs and uses the 5′ cleavage product, a capped-RNA leader (CRL), as primers for transcription. Our previous work demonstrated that RSV snatches CRLs from geminiviral mRNAs in co-infected plants, providing a convenient and powerful approach to map the TSSs of geminiviruses. However, co-infections are not always feasible for all geminiviruses. In this study, we evaluated the use of in vitro cap-snatching of RSV for the same purpose, using tomato yellow leaf curl virus (TYLCV) as an example. We incubated RNA extracted from TYLCV-infected plants with purified RSV ribonucleoproteins in a reaction mixture that supports in vitro cap-snatching of RSV. The RSV mRNAs produced in the reaction were deep sequenced. The CRLs snatched by RSV allowed us to locate 28 TSSs in TYLCV. These results provide support for using RSV’s in vitro cap-snatching to map geminiviral TSSs.

Comparative Genome Analysis of Old World and New World TYLCV Reveals a Biasness toward Highly Variable Amino Acids in Coat Protein.

Begomoviruses, belonging to the family Geminiviridae and the genus Begomovirus, are DNA viruses that are transmitted by whitefly Bemisia tabaci (Gennadius) in a circulative persistent manner. They can easily adapt to new hosts and environments due to their wide host range and global distribution. However, the factors responsible for their adaptability and coevolutionary forces are yet to be explored. Among BGVs, TYLCV exhibits the broadest range of hosts. In this study, we have identified variable and coevolving amino acid sites in the proteins of Tomato yellow leaf curl virus (TYLCV) isolates from Old World (African, Indian, Japanese, and Oceania) and New World (Central and Southern America). We focused on mutations in the coat protein (CP), as it is highly variable and interacts with both vectors and host plants. Our observations indicate that some mutations were accumulating in Old World TYLCV isolates due to positive selection, with the S149N mutation being of particular interest. This mutation is associated with TYLCV isolates that have spread in Europe and Asia and is dominant in 78% of TYLCV isolates. On the other hand, the S149T mutation is restricted to isolates from Saudi Arabia. We further explored the implications of these amino acid changes through structural modeling. The results presented in this study suggest that certain hypervariable regions in the genome of TYLCV are conserved and may be important for adapting to different host environments. These regions could contribute to the mutational robustness of the virus, allowing it to persist in different host populations.

Genetic recombination among tomato yellow leaf curl virus isolates in commercial tomato crops in Kuwait drives emergence of virus diversity: a comparative genomic analysis

ObjectiveWhitefly-transmitted tomato yellow leaf curl virus (TYLCV) continues to be a major constraint to tomato production in Kuwait. However, very limited information is available about the population structure and genetic diversity of TYLCV infecting tomato in Kuwait.ResultsWhole genome sequences of 31 isolates of TYLCV, collected from commercial tomato crops grown in northern (Abdally) and southern (Al Wafra) parts of Kuwait, were deciphered. Eighteen isolates of TYLCV are identified as potential genetic recombinants. The isolates Abdally 6A and Abdally 3B reported in this study were identified to be potential recombinants. Compared to the 15 isolates from the Abdally area, and the three previously reported KISR isolates of Kuwait, six out of sixteen Al Wafra isolates showed an insertion of 19 extra nucleotides near the 5′-end. There are also four nucleotide variations before the 19-extra-nucleotides. The additional 19 nucleotides observed in nine isolates indicate that these isolates might have resulted from a single gene recombination/insertion event. Molecular phylogeny based on complete genome sequences of TYLCV isolates suggests transboundary movement of virus isolates due to geographic proximity. The information presented herein is quite useful for the comprehension of TYLCV biology, epidemiology and would aid in the management of disease in the long run.